TissueEnrich
This is the development version of TissueEnrich; for the stable release version, see TissueEnrich.
All Bioconductor versions of TissueEnrich
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7
Tissue-specific gene enrichment analysis
Bioconductor version: 3.24 · Package version: 1.33.0
The TissueEnrich package is used to calculate enrichment of tissue-specific genes in a set of input genes. For example, the user can input the most highly expressed genes from RNA-Seq data, or gene co-expression modules to determine which tissue-specific genes are enriched in those datasets. Tissue-specific genes were defined by processing RNA-Seq data from the Human Protein Atlas (HPA) (Uhlén et al. 2015), GTEx (Ardlie et al. 2015), and mouse ENCODE (Shen et al. 2012) using the algorithm from the HPA (Uhlén et al. 2015).The hypergeometric test is being used to determine if the tissue-specific genes are enriched among the input genes. Along with tissue-specific gene enrichment, the TissueEnrich package can also be used to define tissue-specific genes from expression datasets provided by the user, which can then be used to calculate tissue-specific gene enrichments.
Author: Ashish Jain [aut, cre], Geetu Tuteja [aut]
Maintainer: Ashish Jain <jain.ashishjain1 at gmail.com>
Citation
From within R, enter citation("TissueEnrich"):
Ashish Jain, Geetu Tuteja. TissueEnrich: Tissue-specific gene enrichment analysis. doi:10.18129/B9.bioc.TissueEnrich, R package version 1.33.0, https://bioconductor.org/packages/TissueEnrich.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("TissueEnrich")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.33.0 |
| License | MIT + file LICENSE |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8 years) |
| Downloads rank | 682 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, GeneSetEnrichment, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/TissueEnrich/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("TissueEnrich")| TissueEnrich: A tool to calculate tissue-specific gene enrichment | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | TissueEnrich_1.33.0.tar.gz |
| Windows binary (x86_64) | TissueEnrich_1.33.0.zip |
| macOS binary (arm64) | TissueEnrich_1.33.0.tgz |
| macOS binary (x86_64) | TissueEnrich_1.33.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TissueEnrich |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TissueEnrich |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 3.5), ggplot2 (>= 2.2.1), SummarizedExperiment (>= 1.6.5), GSEABase (>= 1.38.2)
Imports: dplyr (>= 0.7.3), tidyr (>= 0.8.0), stats